Droplet actuators are used to conduct a wide variety of droplet operations. A droplet actuator typically includes two substrates separated by a droplet operations gap. The substrates include electrodes for conducting droplet operations. The droplet operations gap between the substrates is typically filled with a liquid filler fluid that is immiscible with the fluid that is to be subjected to droplet operations. Droplet operations are controlled by electrodes associated with one or both of the substrates. Components of droplets may in some cases exit the droplets into the filler fluid. From the filler fluid, such components may contaminate other droplets. The invention relates to certain novel approaches to reducing or eliminating the movement of contaminants from one droplet to another on a droplet actuator via liquid filler fluid. In one application, droplet actuators are used to conduct genetic analysis using polymerase chain reaction (PCR) techniques. There is a need for improved methods of performing PCR on a droplet actuator that provide for optimum amplification and detection of a sample target.